To examine the population structure of green turtles in the North Pacific and to improve the estimation of natal origins of the turtles in the foraging grounds, we obtained genome-wide single nucleotide polymorphisms (SNPs) using Multiplexed ISSR Genotyping by sequencing (MIG-seq). Overall nesting population structure observed from genome-wide SNPs was consistent with results from mtDNA. The genome-wide SNPs data was useful to identify the turtles that was more likely to be born in Ogasawara, although they have many candidate natal origins in the western Pacific from mtDNA haplotypes alone. The present results show that analysis based on SNPs data may be an alternative to identify the natal origin of turtles, that there was a limitation on the conventional analysis based on mtDNA data.